A CL-GoDB system was developed as an interface for the Gene Ontology (GO) database and provided a library of functions for manipulating GO. CL-GoDB has been integrated into GOALIE (a bioinformatics software package developed at NYU), which may be used for the study of time course microarray experiments. GOALIE, in its original incarnation, may analyze time course data and search for a Hidden Kripke Model (“HKM”) using a temporal segmentation technique (e.g., one based on information bottleneck based optimization), and may mine the HKM to extract important invariants underlying the experimental data. The HKM may relate to hidden states or possible worlds, transitions among the states, and propositions that label the states. GOALIE may also structure information inherent to HKMs in a Gantt chart format and may provide a visual interface. For example, HKMs or Gantt charts corresponding to, e.g., two related experiments may be compared to discover how their components relate to one another. By comparing Gantt charts using sequence alignment tools, it may be possible to detect aspects of similarity between the two data sets, and hence how “nearby” they are with respect to each other or, e.g., to some other “idealized” experiment. Such distances may also suggest a structure among the datasets (such as a phylogenetic structure) that may be exploited by reflecting it in the structure of the database.